The Doctor's Secret
by jessithefangirl1
Summary: With Amy and Rory gone, the Doctor is having trouble coping. When Sam Winchester asks him for help on Sherlock's new case, it may turn out to be just what the Doctor needed. SUPERWHOLOCK! This contains references to mental illnesses, so it may be triggering to some people. Also, this is my first time with fanfiction, so feedback would be great!


**The Doctor's Secret**

As the whirling noise of the TARDIS died down, the Doctor hesitantly walked to the door, pushing down his sleeved over his aching arms. "Conceal, don't feel" popped into his head, and he smirked to himself at the irony. One of the last adventures he has with the Ponds was to a fly-in theater near Neptune. It was Amy's birthday, and the Doctor knew how much she loved Disney princess movies. "I can never resist a good fairytale," she always used to say, winking at him.

The Doctor sighed, his heart suddenly heavy. It had been about eleven years since Manhattan, and it still felt as though he had just watched Amy being zapped back in time, where she was forever unreachable. His Amelia Pond, gone. A sudden feeling of despair began to rise from his stomach, creeping into his chest. It felt as though cold, dead fingers were reaching up, trying to grip his hearts. Usually the Doctor would let the panic wash over him, wracking his body in waves. Snot and tears would become muddled on his face, and his eyes would turn into a raw red, causing his irises to look a magnificent green. Fear and despair would take its hold in his chest and tear a gaping hole, leaving him feeling hollow and numb. These were the times when the Doctor gave into his new habit.

Not having time to break down, he closed his eyes and took deep breaths, stifling his oncoming anxiety. It slowly crept back into the pit of his stomach, leaving the Doctor in peace for the time being. Tugging his sleeves down once more, he opened the door and stepped out into the London air.

He glanced around briefly and spotted an overgrown man shifting from foot to foot. He wore a leather jacket with jeans and kept adjusting the shirt underneath. Gathering his composure, fixing his bow tie, and pasting a smile on his face, the Doctor strode towards the man. "Sam Winchester!" He yelled as he neared the man. "The human moose!"

Sam's head jerked up, his hair uncovering his angled face. As his liquid brown eyes landed on the Doctor, his face broke out into a relieved grin. "Doctor!" He boomed. "You scared me for a minute there. I thought you were Crowley, with the accent and name-calling." He held out his enormous hand.

The Doctor took it and shook gingerly, not wanting to expose his arm. "Please tell me that little dalek isn't here." The thought of Crowley made him wish he carried a weapon; their last encounter had ended with the Doctor leaping across the table and grabbing the demon by the throat.

Sam smirked, seemingly reading his thoughts. "No, he's not. Don't worry, I wouldn't have signaled you here if he was."

"Ah, then you have more decency than your brother." He paused, glancing at his surroundings. The TARDIS has landed right outside a little shop named Speedy's. The buildings along Baker Street were white stone on the first floor and a dark brick on the top. Black doors were dispersed evenly with windows in between. The particular door they were standing in front of had "221B" in gold letters, just above the knocker. "Why did you signal me? And why're you here? I thought your area was the States, not England. Did Sherlock get himself into trouble again?"

Sam shook his head. "No, not this time. He has a strange case that he can't explain, so he called me and Dean. Took us about a week to figure out this thing isn't from Earth. Despite what people seem to think, we're not exactly Scully and Mulder."

The Doctor nodded his head and gazed across the street at a little redheaded girl tugging along a small dog. Her face was twisted in frustration, reminding him of little Amelia, the first time they met. She became so perplexed with him when he kept spitting out food in disgust.

His anxiety began to creep out of its hiding spot again. The Doctor crosses his arms and dug his fingers into them. The pain provided relief and he looked back at Sam, who was watching him carefully. "Well, where is everyone?" He finally asked.

Same squinted at the Doctor for a moment until he finally shrugged his shoulders and answered, "Sherlock and John went to question Mycroft. Dean and Cas are upstairs, trying to dig up any info."

"Well then, shall we go help?" The Doctor turned towards the door and opened it. A wave of smells hit him as he stepped through the threshold. The musky scent of Sherlock's study mixed rather pleasantly with the small of Mrs. Hudson's baking and tea.

Sam walked in and quietly shut the door. From the upstairs flat, they could hear Cas and Dean discussing the case.

The Doctor suddenly turned to Sam. "Did you tell them you contacted me?"

"Yeah, I did. Dean wasn't too happy about it at first, but once Cas agreed, he seemed okay with it." The Doctor nodded at this and preceded up the stairs, Sam following behind him. He opened the door to the flat and surveyed it. Castiel sat on the couch against the wall with his nose buried in a book. Although he was inside, he kept his signature trench coat on. Dean sat at Sherlock's desk, a laptop in front of him and a coffee beside it. Judging by the smell of it, it contained some sort of alcohol. He wore a dark green plaid shirt over a loose grey t-shirt with his usual jeans and boots. Leaning back in his chair with his hands behind his head, he glared at the laptop screen. It looked as if he was in the first stages of defeat.

When the Doctor stepped into the room, they both looked up. Castiel's blue eyes pierced the Doctor, detecting that something was terribly wrong. Dean gazed at him with glazed over green eyes, nodded, and returned to his position. Castiel, however, continued to stare, trying to see beyond the Doctor's façade. Fearing that he would make a comment, the Doctor held his breath. After a few intense heart beats, Castiel gave a little smile and muttered "Doctor" before returning to his book.

The Doctor let out a silent sigh of relief and went to sit down in John's chair. Sam walked in, closed the door, and turned to the others. "Find anything?"

Castiel shook his head without looking up, and Dean snarled, "Not a damn thing."

Sam nodded. "Right then," he said, turning to the Doctor. "Basically what's been happening is people are disappearing and very few bodies have been found. Only, I don't know if I'd even call them bodies…" His eyes studied the floor as he tried to find the right words. Struggling, he continued, "They seem to only be skins. No organs, no blood, no bone or muscle, nothing except skin. We're never seen anything like not, not even Cas."

The Doctor nodded, knowing exactly what they were dealing with. "What sorts of people is this happening to?"

"At first, it was normal people, but recently, it's been happening to government officials."

The Doctor let out a humorless laugh. "And to think I believed I was done with you," he muttered. He leaned forward and rested his forearms on this knees, studying his clasped hands.

"What was that?" Dean spoke up rather impatiently. He studied the Doctor with suspicious eyes. He never like the time lord, always distrusting his ridiculous logic and his odd way of moving about. In the ten years he had known him, he had never seen him with anyone, whether it was a friend or family member or something more. In Dean's eyes, people who didn't keep family close were hiding something.

The Doctor sighed and leaned back. "The Sliveen. I dealt with them before, back in 2005. For me, that was near a century ago, a couple of regenerations back. If they're taking government officials, they're planning something, and it may very well mean the end of the world." The Doctor glanced up and grimaced. "I'm guessing you want me to stick around and help?"

"Just tell us how to kill them, and you can fly away in your little blue box," Dean snarled.

"No," the Doctor replied harshly. "I can talk some sense into them, there's no need for a blood bath. I've done it before, I can do it again."

Sam quickly clasped his hands together before Dean could protest. "Great! That solves the problem then. Doctor when do you-" The phone in his pocket began playing "Carry On Wayward Son," interrupting him. He checked the screen and answered, "Sherlock? Yeah, I'm still at the flat… No, we haven't found anything, but-" His eyebrows suddenly pulled down over his eyes. "You WHAT?! Goddammit, Sherlock… Yeah, we'll be there soon." He pressed the end button in frustration. "Those two idiots, I swear to fuck. Cas, let's go." Dean start to get up to leave with them, but Sam stopped him. "Sherlock wants you to stay here, he says you're too much like Anderson.

Dean's face twisted into an enraged look. "What, and leave me with him?" He said while pointing at the Doctor.

Offended, the Doctor spoke up, "Oi, it's because of your stupidity and lack of knowledge that I'm here."

"You son of a bitch," Dean growled as he started towards the Doctor. Suddenly, Castiel appeared in front of him, blacking his way.

"DEAN!" He yelled, "We need him or the world will end! So quit acting like a selfish bastard and think about the human race." His deep voice boomed throughout the flat, causing the others to stare at him, startled.

Quickly overcoming his initial surprise, Dean pressed his lips together and nodded curtly. "Fine," he mumbled and went back to sit at the desk.

"Well…now that that's settled, we need to leave." Sam turned towards the door and left, followed by Castiel. Silence filled the flat in their absence.

The Doctor, still dismayed by at the incident, began to absentmindedly scratch at his arm. Dean fixed his eyes on the laptop again.

Lost in thought, the Doctor didn't realize his actions until he felt a sharp pain. Startled, he gasped, earning an annoyed glance from Dean. Quickly recovering, he smiled and looked straight ahead, hoping Dean would ignore him. Luck was obviously not on his side.

"What'd you do to your arm?" He inquired, more curious than concerned.

"It's nothing, just a scratch," the Doctor tried to shrug it off. Dean studied him and got up. Moving towards him, he held out his hand.

"Here, let me see," he sighed, thinking the old fool didn't know how to bandage a wound.

The Doctor began squirming, attempting to hide his arm. No, that's not necessary. I'm fine, really." Before he could escape from the chair, Dean was standing over him, grabbing for his arm.

"Doctor, quit being stupid. I just want to make sure it's not infected." He clenched his jaw in frustration, struggling with the Doctor. He got a hold on his upper arm and grabbed his wrist. The Doctor yelped in pain and tried to tu his arm back, but Dean was too strong.

"Dean! Stop!" He cried as Dean grabbed his sleeve. His arm burned with pain, having been contorted and irritated in the struggle. _No, no, no,_ he though as Dean pushed up the sleeve, revealing the Doctor's arm.

Dean studied his arm, confused at first. But as realization hit him, a seed of revulsion grew in the pit of his stomach.

Deep, long cuts covered the Doctor's inner forearm. They were all inflamed from the skirmish, and many of them were oozing think red blood. Dean's eyes widened as the thought of the Doctor doing this to himself crossed his mind. He suddenly felt dizzy at the sight of twenty-two gaping wounds.

Sensing Dean loosening his grip, the Doctor yanked his arm away and hurridly pushed down his sleeve. Seeing the look of disgust on Dean's face, he knew what was coming next. The accusations, the insults. Reactions were always the worst when it came to this. "You shouldn't have done that," he said quietly.

Dean looked at his with sudden regret in his eyes. "Doctor… What happened?" He slowly straightened up and sat in Sherlock's chair. He stared intently at the Doctor, genuinely concerned.

The Doctor studied Dean's face for a moment, searching for signs of insincerity or mockery. Not finding anything of the he sighed and studied his hands. "When you get to be as old as me, you lose everyone you've ever loved at one point. And eventually one shatters your heart, or hearts in my case. My last two companions… Amy and Rory Williams. The Ponds." A flash of pain crossed his face and tears welled up in his eyes. It had been quite a while since he had said those names out loud. Clearing his throat, he continued, "They were the closest thing I have ever had to a family. I watch Amy grow up…in a way. I watched her and Rory get married and have a beautiful baby girl. I eventually fell in love and married their daughter. We're both time travelers," he added when he saw Dean's confused look. "Amy was the first face this face saw. She became seared into my hearts, and I thought she would be with me til the end of my days. And now her and Rory have been gone for eleven years. Something in me broke, and now this…" he lifted his arm, "this is the only way I can deal with the pain." He looked up at Dean, trying to gauge his reaction. His face was blank, giving nothing away, but he was studying the Doctor.

Finally, nodded his head as if coming to a decision, and he sat back. "I have to tell the others when they get back," he stated.

"No!" The Doctor exclaimed. He took a deep breath. "No, please. At least wait until the ordeal with the Sliveen is take care of," he pleaded.

Dean looked out the window, thinking. The Doctor held his breath as he watched Dean contemplate the situation. After a minute or two, he sighed. Before he could get his answer out, the front door slammed, and voices drifted up to the flat. At least four pairs of feet pounded up the stairs. Sherlock and Castiel stormed into the room, apparently in a heated argument.

"Trust me, I knew what I was doing," Sherlock insisted in a bored voice.

"Obviously not if I had to revive him, and he's still not sober!" Castiel retorted.

As if to prove his point, Sam stumbled in with John slung over his shoulders, lips pressed together and shaking his head. On the other hand, John seemed to be enjoying himself with a sheepish grin on his face and his eyes half closed. As Sam gingerly set him on the couch, he slurred, "Why thank ya, Sammy boy. You are shuch a good moosh. Good, good moosh, yesh you…" His last sentence was lost as he fell asleep. Sam rolled his eyes and hurried into the kitchen.

The Doctor and Dean sat and observed the commotion, neither wanting to get caught up in it. Castiel and Sherlock were still arguing over John.

Sam returned to John with water and a wet towel. "Dean, can you help? Sherlock decided to use John as an experiment," he said, glaring at Sherlock.

"Well, he proved my thesis to be correct, and he gave me more information concerning a case. So I have no regrets," Sherlock informed Sam.

"And killed him in the process. Dean, get over here."

Dean got up, shaking his head and biting back laughter. As he passed the Doctor, he patted his shoulder and muttered "okay" before going to help Sam.

The Doctor smiled to himself in relief. His secret was safe with Dean for now. His attention returned back to Castiel and Sherlock, rather enjoying their debate on Sherlock's ethics. For the first time in years, the Doctor was content to be around human shenanigans once again.


End file.
